Lt. Col. Christopher O’Melia was relieved of command of 1st Battalion, 4th Marine Regiment, by the commanding general of 1st Marine Division.
The hospital where the Marines were sent had been planning a mass-casualty response training for the day of the real-life emergency.
The island of Mindanao has been reeling from the effects of heavy rain, displacing an estimated 795,000 people.
It was an "isolated incident and there was no threat to other Marines or the public,” a Marine spokeswoman said.
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